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Analytical and Bioanalytical Chemistry Oct 2023Emerging polycyclic aromatic nitrogen heterocycles (PANHs) contributes significantly to the health risk associated with inhaling polluted air. However, there is a lack...
Emerging polycyclic aromatic nitrogen heterocycles (PANHs) contributes significantly to the health risk associated with inhaling polluted air. However, there is a lack of analytical methods with the needed performance to their determination. This study presents the optimization and validation for the first time of a green microscale extraction procedure for the determination of twenty-one PANHs, including carbazole, indole, and quinolone classes, in particulate matter (PM) samples by gas chromatography-mass spectrometry. A simplex-centroid mixture design and full factorial design (2) were employed to optimize the following extraction parameters: type and volume of solvent, sample size, extraction time, and necessity of a cleanup step. Low limits of detection and quantification (LOD < 0.97 pg m and LOQ < 3.24 pg m, respectively) were obtained in terms of matrix-matched calibration. The accuracy and precision of the method were adequate, with recoveries in three levels between 73 to 120% and intraday and interday relative standard deviations from 2.0 to 12.9% and 7.3 to 18.9%, respectively. The green character of the method was evaluated using the Analytical Greenness (AGREE) tool, where a score of 0.69 was obtained, indicating a great green procedure. The method was applied to PM samples collected from sites with different characteristics; the concentrations ranged from 69.3 pg m (2-methylcarbazole) to 11,874 pg m (carbazole) for individual PANHs and from 2306 to 24,530 pg m for ∑21PANHs. Principal component analysis (PCA) and hierarchical clustering enabled discrimination of the sampling sites according to the PANHs concentrations. The score plots formed two distinct groups, one with samples containing higher concentrations of PANHs, corresponding to sites with a major influence from diesel emissions, and another group with minor PANH contents, corresponding to sites impacted by emissions from urban traffic and industrial activities.
PubMed: 37541975
DOI: 10.1007/s00216-023-04889-z -
G3 (Bethesda, Md.) Dec 2023Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop...
Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.
Topics: Humans; Genome-Wide Association Study; Plant Breeding; Chromosome Mapping; Phenotype; Genotype
PubMed: 37963231
DOI: 10.1093/g3journal/jkad216 -
Diagnostics (Basel, Switzerland) Oct 2023The study aims to develop a decision pathway based on HEAR score and 0 h high-sensitivity cardiac troponin T (hs-cTnT) to safely avoid a second troponin test for...
The study aims to develop a decision pathway based on HEAR score and 0 h high-sensitivity cardiac troponin T (hs-cTnT) to safely avoid a second troponin test for suspected non-ST elevation myocardial infarction (NSTEMI) in emergency departments. A HEAR score consists of history, electrocardiogram, age, and risk factors. A HEAR pathway is established using a Bayesian approach based on a predefined safety threshold of NSTEMI prevalence in the rule-out group. In total, 7131 patients were retrospectively enrolled, 582 (8.2%) with index visit NSTEMI and 940 (13.2%) with 180-day major adverse cardiovascular events (MACE). For patients with a low-risk HEAR score (0 to 2) and low 0 h hs-cTnT (<14 ng/L), the HEAR pathway recommends early discharge without further testing. After the HEAR pathway had been applied to rule out NSTEMI, the negative predictive value of index visit NSTEMI was 100.0% (95% CI, 99.8% to 100.0%) and false-negative rate of 180-day MACE was 0.40% (95% CI, 0.18% to 0.87%). Compared with the 0 h hs-cTnT < limit of detection (LoD) strategy (<5 ng/L), the HEAR pathway could correctly reclassify 1298 patients without MACE as low risk and lead to a 18.2% decrease (95% CI, 17.4-19.1%) in the need for a second troponin test. The HEAR pathway may lead to a substantial and safe reduction in repeated troponin test for emergency department patients with suspected NSTEMI.
PubMed: 37892038
DOI: 10.3390/diagnostics13203217 -
Ear and HearingA multisite clinical trial was conducted to obtain cochlear implant (CI) efficacy data in adults with asymmetric hearing loss (AHL) and establish an evidence-based...
OBJECTIVE
A multisite clinical trial was conducted to obtain cochlear implant (CI) efficacy data in adults with asymmetric hearing loss (AHL) and establish an evidence-based framework for clinical decision-making regarding CI candidacy, counseling, and assessment tools. Study hypotheses were threefold: (1) 6-month postimplant performance in the poor ear (PE) with a CI will be significantly better than preimplant performance with a hearing aid (HA), (2) 6-month postimplant performance with a CI and HA (bimodal) will be significantly better than preimplant performance with bilateral HAs (Bil HAs), and (3) 6-month postimplant bimodal performance will be significantly better than aided, better ear (BE) performance.
DESIGN
Forty adults with AHL from four, metropolitan CI centers participated. Hearing criteria for the ear to be implanted included (1) pure-tone average (PTA, 0.5, 1, 2 kHz) of >70 dB HL, (2) aided, monosyllabic word score of ≤30%, (3) duration of severe-to-profound hearing loss of ≥6 months, and (4) onset of hearing loss ≥6 years of age. Hearing criteria for the BE included (1) PTA (0.5, 1, 2, 4 kHz) of 40 to 70 dB HL, (2) currently using a HA, (3) aided, word score of >40%, and (4) stable hearing for the previous 1-year period. Speech perception and localization measures, in quiet and in noise, were administered preimplant and at 3-, 6-, 9-, and 12-months postimplant. Preimplant testing was performed in three listening conditions, PE HA, BE HA, and Bil HAs. Postimplant testing was performed in three conditions, CI, BE HA, and bimodal. Outcome factors included age at implantation and length of deafness (LOD) in the PE.
RESULTS
A hierarchical nonlinear analysis predicted significant improvement in the PE by 3 months postimplant versus preimplant for audibility and speech perception with a plateau in performance at approximately 6 months. The model predicted significant improvement in postimplant, bimodal outcomes versus preimplant outcomes (Bil HAs) for all speech perception measures by 3 months. Both age and LOD were predicted to moderate some CI and bimodal outcomes. In contrast with speech perception, localization in quiet and noise was not predicted to improve by 6 months when comparing Bil HAs (preimplant) to bimodal (postimplant) outcomes. However, when participants' preimplant everyday listening condition (BE HA or Bil HAs) was compared with bimodal performance, the model predicted significant improvement by 3 months for localization in quiet and noise. Lastly, BE HA results were stable over time; a generalized linear model analysis revealed bimodal performance was significantly better than performance with a BE HA at all postimplant intervals for most speech perception measures and localization.
CONCLUSIONS
Results revealed significant CI and bimodal benefit for AHL participants by 3-months postimplant, with a plateau in CI and bimodal performance at approximately 6-months postimplant. Results can be used to inform AHL CI candidates and to monitor postimplant performance. On the basis of this and other AHL research, clinicians should consider a CI for individuals with AHL if the PE has a PTA (0.5, 1, 2 kHz) >70 dB HL and a Consonant-Vowel Nucleus-Consonant word score ≤40%. LOD >10 years should not be a contraindication.
Topics: Adult; Humans; Cochlear Implants; Prospective Studies; Cochlear Implantation; Hearing Loss; Hearing Aids; Speech Perception; Treatment Outcome
PubMed: 37018114
DOI: 10.1097/AUD.0000000000001354 -
NPJ Genomic Medicine Aug 2023Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive...
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
PubMed: 37580330
DOI: 10.1038/s41525-023-00364-x -
Journal of Neuroengineering and... Mar 2024Effective stroke rehabilitation requires high-dose, repetitive-task training, especially during the early recovery phase. However, the usability of upper-limb...
BACKGROUND
Effective stroke rehabilitation requires high-dose, repetitive-task training, especially during the early recovery phase. However, the usability of upper-limb rehabilitation technology in acute and subacute stroke survivors remains relatively unexplored. In this study, we introduce subacute stroke survivors to MyoGuide, a mobile training platform that employs surface electromyography (sEMG)-guided neurofeedback training that specifically targets wrist extension. Notably, the study emphasizes evaluating the platform's usability within clinical contexts.
METHODS
Seven subacute post-stroke patients (1 female, mean age 53.7 years, mean time post-stroke 58.9 days, mean duration per training session 48.9 min) and three therapists (one for eligibility screening, two for conducting training) participated in the study. Participants underwent ten days of supervised one-on-one wrist extension training with MyoGuide, which encompassed calibration, stability assessment, and dynamic tasks. All training records including the Level of Difficulty (LoD) and Stability Assessment Scores were recorded within the application. Usability was assessed through the System Usability Scale (SUS) and participants' willingness to continue home-based training was gauged through a self-developed survey post-training. Therapists also documented the daily performance of participants and the extent of support required.
RESULTS
The usability analysis yielded positive results, with a median SUS score of 82.5. Compared to the first session, participants significantly improved their performance at the final session as indicated by both the Stability Assessment Scores (p = 0.010, mean = 229.43, CI = [25.74-433.11]) and the LoD (p < 0.001; mean: 45.43, CI: [25.56-65.29]). The rate of progression differed based on the initial impairment levels of the patient. After training, participants expressed a keen interest in continuing home-based training. However, they also acknowledged challenges related to independently using the Myo armband and software.
CONCLUSIONS
This study introduces the MyoGuide training platform and demonstrates its usability in a clinical setting for stroke rehabilitation, with the assistance of a therapist. The findings support the potential of MyoGuide for wrist extension training in patients across a wide range of impairment levels. However, certain usability challenges, such as donning/doffing the armband and navigating the application, need to be addressed to enable independent MyoGuide training requiring only minimal supervision by a therapist.
Topics: Humans; Female; Middle Aged; Wrist; Stroke; Stroke Rehabilitation; Upper Extremity; Wrist Joint
PubMed: 38515192
DOI: 10.1186/s12984-024-01334-9 -
Tropical Biomedicine Sep 2023Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including...
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including Indian subcontinent and Southeast Asia. A proper diagnostic tool for early diagnosis of CHIKV infection is crucial to facilitate patient management and control virus transmission at the earliest stage of outbreak. Therefore, a TaqMan minor groove binder (MGB) probe-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay was developed to detect and quantify the CHIKV. The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. The nucleotide mismatches of primers and probe with 730 global CHIKV sequences and 13 alphaviruses were then analysed in silico. In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming. In silico analysis revealed that the critical regions of primers and probe were at least 99.6% matched with the 730 global CHIKV sequences. Besides, the primers and probe showed at least 5/20 (25.0%) and 4/17 (23.5%) nucleotide mismatches with 13 alphaviruses respectively. The amplification efficiency of qRT-PCR assay was 100.59% (95% CI= 93.06, 109.33) with a R score of 0.957. Its limit of detection (LOD) at 95% probability level was 16.6 CHIKV RNA copies (95% CI= 12.9, 28.9). The qRT-PCR assay was specific to CHIKV without cross-reacting with all dengue virus serotypes, Getah virus, Tembusu virus and Zika virus. The diagnostic results of qRT-PCR assay were perfectly agreed (k=1.000, p=0.003) with a commercial trioplex assay, with sensitivity of 100% (95% CI= 61, 100) and specificity of 100% (95% CI= 44, 100). Overall, the developed qRT-PCR assay is ideal for rapid, sensitive and specific detection as well as quantification of CHIKV.
Topics: Animals; Humans; Chikungunya virus; Reverse Transcription; Sensitivity and Specificity; Reverse Transcriptase Polymerase Chain Reaction; Zika Virus; DNA Primers; Nucleotides; Zika Virus Infection; Real-Time Polymerase Chain Reaction; RNA, Viral
PubMed: 37897164
DOI: 10.47665/tb.40.3.007 -
Talanta Aug 2023High concentrations of inorganic arsenic in groundwater for human consumption is a worldwide common problem. Particularly, the determination of As(III) becomes...
High concentrations of inorganic arsenic in groundwater for human consumption is a worldwide common problem. Particularly, the determination of As(III) becomes important, since this species is more toxic than organic, pentavalent and elemental arsenic forms. In this work, a 3D-printed device that included a 24-well microplate was developed to perform the colourimetric kinetic determination of arsenic (III) by digital movie analysis. A smartphone camera attached to the device was used to take the movie during the process where As(III) inhibited the decolourization of methyl orange. The movie images were subsequently transformed from RGB to YIQ space to obtain a new analytical parameter called "d", which was related to the chrominance of the image. Then, this parameter allowed the determination of the inhibition time of reaction (t), which was linearly correlated with the concentration of As(III). A linear calibration curve (R = 0.9995) in the range from 5 μg L to 200 μg L was obtained. The method was precise (RSD = 1.2%), and the limits of detection (LOD) and quantification (LOQ) were 1.47 μg L and 4.44 μg L, respectively. These values were lower than the limit established by the World Health Organization for total arsenic in drinking water (10 μg L). The accuracy of the method was assessed by a recovery study with optimal results (94.3%-104.0%). Additionally, the Analytical GREEnness metric approach was applied, obtaining a score 1.7 times higher than previously published works. The method is simple, portable and low-cost, being in compliance with various principles of green analytical chemistry.
PubMed: 37201338
DOI: 10.1016/j.talanta.2023.124625 -
The Analyst Oct 2023Polycyclic aromatic hydrocarbons (PAHs) have attracted a lot of environmental concern because of their carcinogenic and mutagenic properties, and the fact they can...
Polycyclic aromatic hydrocarbons (PAHs) have attracted a lot of environmental concern because of their carcinogenic and mutagenic properties, and the fact they can easily contaminate natural resources such as drinking water and river water. This study presents a simple and sensitive point-of-care SERS detection of PAHs combined with machine learning algorithms to predict the PAH content more precisely and accurately in real-life samples such as drinking water and river water. We first synthesized multibranched sharp-spiked surfactant-free gold nanostars (GNSs) that can generate strong surface-enhanced Raman scattering (SERS) signals, which were further coated with cetyltrimethylammonium bromide (CTAB) for long-term stability of the GNSs as well as to trap PAHs. We utilized CTAB-capped GNSs for solution-based 'mix and detect' SERS sensing of various PAHs including pyrene (PY), nitro-pyrene (NP), anthracene (ANT), benzo[a]pyrene (BAP), and triphenylene (TP) spiked in drinking water and river water using a portable Raman module. Very low limits of detection (LOD) were achieved in the nanomolar range for the PAHs investigated. More importantly, the detected SERS signal was reproducible for over 90 days after synthesis. Furthermore, we analyzed the SERS data using artificial intelligence (AI) with machine learning algorithms based on the convolutional neural network (CNN) model in order to discriminate the PAHs in samples more precisely and accurately. Using a CNN classification model, we achieved a high prediction accuracy of 90% in the nanomolar detection range and an f1 score (harmonic mean of precision and recall) of 94%, and using a CNN regression model, achieved an RMSE = 1.07 × 10 μM. Overall, our SERS platform can be effectively and efficiently used for the accurate detection of PAHs in real-life samples, thus opening up a new, sensitive, selective, and practical approach for point-of-need SERS diagnosis of small molecules in complex practical environments.
PubMed: 37671999
DOI: 10.1039/d3an00636k -
The Plant Genome Dec 2023Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine...
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
Topics: Quantitative Trait Loci; Zinc; Plant Breeding; Fabaceae; Iron
PubMed: 37408143
DOI: 10.1002/tpg2.20361